NUPACK: Analysis and design of nucleic acid systems

: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: • Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. • Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium. • Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. © 2010 Wiley Periodicals, Inc. J Comput Chem 32: 170–173, 2011 Key words: RNA; DNA; complexes; concentrations; sequence design

• Type: Journal
• Year: 2011
• Where: JCC
• Authors: Joseph N. Zadeh, Conrad Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, Niles A. Pierce
• Keywords: JCC 2011, Nucleic Acid, Nucleic Acid Package, Nucleic Acid Strands